human-gut-profiler.ngl

#!/usr/bin/env ngless
ngless "0.9"
import "mocat" version "0.0"
import "igc" version "0.9"
local import "motus" version "2.5"

input = load_mocat_sample(ARGV[1])
RESULTS = ARGV[2]

qc_reads = preprocess(input, keep_singles=False) using |read|:
    read = substrim(read, min_quality=25)
    if len(read) < 45:
        discard

human_mapped = map(qc_reads, reference='hg19')

non_human = select(human_mapped) using |mr|:
    mr = mr.filter(min_match_size=45, min_identity_pc=90, action={unmatch})
    if mr.flag({mapped}):
        discard

non_human_reads = as_reads(non_human)

igc_mapped = map(non_human_reads, reference='igc', mode_all=True)
igc_mapped_post = select(igc_mapped) using |mr|:
    mr = mr.filter(min_match_size=45, min_identity_pc=95, action={drop})
    if not mr.flag({mapped}):
        discard

igc_counts = count(igc_mapped_post,
                   features=['OGs'],
                   multiple={dist1},
                   normalization={scaled})
write(igc_counts,
      ofile=RESULTS </> 'eggNOG.traditional.counts.txt',
      auto_comments=[{hash}, {script}])

motus_counts = motus(non_human_reads, sample=ARGV[1])

write(motus_counts,
      ofile=RESULTS </> 'motus_and_specI.counts.txt')